Biology subjects

Singh, R.

Publications and source records attributed to Singh, R..

14 recordsLinked to original sources

bioRxiv2018

Draft genome of the liver fluke Fasciola gigantica

Fascioliasis is a neglected food-borne disease caused by liver flukes (genus Fasciola) and affects more than 200 million people worldwide. Despite technological advances, little is known about the molecular biology and biochemistry of the fluke. We present the draft genome of Fasciola gigantica for the first time. The assembled draft genome has a size of ~1.04 Gb with an N50 of 129 kb. A total of 20,858 genes were predicted. The de novo repeats identified in the draft genome were 46.85%. In pathway analysis, all the genes of glycolysis, Krebs cycle and fatty acid metabolism were found to be present, but the key genes for fatty acid production in fatty acid biosynthesis were missing. This indicates that the fatty acid required for the survival of the fluke may be acquired from the host bile. The genomic information will provide a comprehensive resource to facilitate the development of novel interventions for fascioliasis control.

bioinformatics↗

bioRxiv2018

Antifungal effects of 3-(4-Phenyl-thiazol-2-yl)-2-thioxo-2, 3-dihydro-1H-quinazolin-4-one against Aspergillus Species

Aspergillus infections have become an important health problem with the increasing number of patients. Available antifungal drugs are lack with their spectrum, toxic or immunosuppressive in nature, so that need to develop new compound with high efficacy. To evaluate antifungal efficacy of synthesized compound and to identify the protein profile of Aspergillus fumigatus treated with antifungal. Clinical isolates of A. fumigatus, A. flavus and A. niger were cultured and efficacy of compound were conducted by Disc Diffusion Assay (DDA), Microbroth Dilution Assay (MDA). Percent of spore germination inhibition assay (PSGI), Time kill analysis and toxicity assay. The culture filtrate containing secretory proteins was collected after 24 h growth and expression of downregulated proteins were identified. We developed a new and useful quinazoline derivatives expected to antifungal activity. The result of anti-Aspergillus evolution revealed that one of the 3-(4-Phenyl-thiazol-2-yl)-2-thioxo-2, 3-dihydro-1H-quinazolin-4-one (DDVKT4Q) exhibited appreciable activity. The potency of compound was found concentration of 3.125 {micro}g/disc by disc diffusion assay (DDA) and 15.625 {micro}g/ml. by Microbroth Dilution Assay (MDA). The compound was nontoxic up to concentration 625 {micro}g/ml and its lysed only 35.9% of human erythrocytes, at the highest dose tested. Its observed that the treatment of pathogen with DDVKT-4Q targeted the expression of four proteins having molecular weights 18 kDa 37 KDa and 43 KDa proteins was completely inhibited or down regulated by the compound the extra cellular. The novel compound DDVKT-4Q, having antifungal activity Can be exploited further to develop new ideal antimycotic drugs.

microbiology↗

bioRxiv2018

Resumption of spermatogenesis in senescent goldfish Carassius auratus (Linnaeus, 1758) through spermatogonial cell therapy

In recent times, stem cell research has gained considerable prominence because of its applications in assisted reproductive technology and the treatment of deadly diseases. In teleost fishes, spermatogonial stem cells have been effectively used to produce progeny of difficult-to-breed fish species and/or commercially valuable species through the surrogacy technique. The present study is the first report of an innovative application of stem cell therapy in teleostean fish species for revitalising the reproductive competence of senescent individuals. Senescent male goldfish, Carassius auratus aged approximately 10 years were procured from an ornamental fish-breeding farm and were reared locally for an additional 2 years. The senescence of the fish was evaluated and confirmed using histological analysis, gonadal index assessment, and germ-cell specific vasa gene expression. Analyses revealed the absence of spermatogonial cells and other germ cells in the testes of the senescent fish (n = 5). Spermatogonial cells from a prepubertal C. auratus male donor were isolated using discontinuous percoll gradients, labelled with the fluorescent dye PKH-26, and transplanted into the gonads of senescent C. auratus males through the urogenital papilla. Six months after the therapy, spermatozoa from males were collected through applying gentle manual pressure on the abdomen and were observed under the microscope. All the senescent therapy-treated C. auratus males produced spermatozoa from the transplanted cells; this was confirmed by retention of PKH-26 in the spermatozoa and diagnostic SSR locus. The senescent males were crossed with gravid C. auratus females through artificial insemination and natural spawning, and viable progeny was produced. These observations suggest that the reproductive competence of senescent individuals of commercially valuable and/or endangered fish species can be revitalised and extended through spermatogonia stem cell therapy to produce functional gametes.

developmental biology↗

bioRxiv2018

Use of Hyperspectral Reflectance-Derived Relationship Matrices for Genomic Prediction of Grain Yield in Wheat

Hyperspectral reflectance phenotyping and genomic selection are two emerging technologies that have the potential to increase plant breeding efficiency by improving prediction accuracy for grain yield. Hyperspectral cameras quantify canopy reflectance across a wide range of wavelengths that are associated with numerous biophysical and biochemical processes in plants. Genomic selection models utilize genome-wide marker or pedigree information to predict the genetic values of breeding lines. In this study, we propose a multi-kernel GBLUP approach to genomic selection that uses genomic marker-, pedigree-, and hyperspectral reflectance-derived relationship matrices to model the genetic main effects and genotype x environment (G x E) interactions across environments within a bread wheat (Triticum aestivum L.) breeding program. We utilized an airplane equipped with a hyperspectral camera to phenotype five differentially managed treatments of the yield trials conducted by the Bread Wheat Improvement Program, International Maize and Wheat Improvement Center (CIMMYT) at Ciudad Obregon, Mexico over four breeding cycles. We observed that single-kernel models using hyperspectral reflectance-derived relationship matrices performed similarly or superior to marker-and pedigree-based genomic selection models when predicting within and across environments. Multi-kernel models combining marker/pedigree information with hyperspectral reflectance phentoypes had the highest prediction accuracies; however, improvements in accuracy over marker-and pedigree-based models were marginal when correcting for days to heading. Our results demonstrates the potential of hyperspectral imaging in predicting grain yield within a multi-environment context, it also supports further studies on integration of hyperspectral reflectance phenotyping in breeding programs.

genomics↗

bioRxiv2018

Bacterial and fungal contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin-, cellulose-and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of 13C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose-degradation. Very few taxa incorporated 13C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation. Variation in lignin-degrading activity was better explained by microbial community properties, such as catabolic gene content and community structure, than cellulose-degrading activity. SIP significantly improved shotgun metagenome assembly resulting in the recovery of several high-quality draft metagenome-assembled genomes and over 7,500 contigs containing unique clusters of carbohydrate-active genes. These results improve understanding of which organisms, conditions and corresponding functional genes contribute to lignocellulose decomposition.

molecular biology↗

bioRxiv2018

Attend and Predict: Understanding Gene Regulation by Selective Attention on Chromatin

The past decade has seen a revolution in genomic technologies that enabled a flood of genome-wide profiling of chromatin marks. Recent literature tried to understand gene regulation by predicting gene expression from large-scale chromatin measurements. Two fundamental challenges exist for such learning tasks: (1) genome-wide chromatin signals are spatially structured, high-dimensional and highly modular; and (2) the core aim is to understand what the relevant factors are and how they work together. Previous studies either failed to model complex dependencies among input signals or relied on separate feature analysis to explain the decisions. This paper presents an attention-based deep learning approach, AttentiveChrome, that uses a unified architecture to model and to interpret dependencies among chromatin factors for controlling gene regulation. AttentiveChrome uses a hierarchy of multiple Long Short-Term Memory (LSTM) modules to encode the input signals and to model how various chromatin marks cooperate automatically. AttentiveChrome trains two levels of attention jointly with the target prediction, enabling it to attend differentially to relevant marks and to locate important positions per mark. We evaluate the model across 56 different cell types (tasks) in humans. Not only is the proposed architecture more accurate, but its attention scores provide a better interpretation than state-of-the-art feature visualization methods such as saliency maps.1

bioinformatics↗

bioRxiv2018

GaKCo: a Fast GApped k-mer string Kernel using COunting

String Kernel (SK) techniques, especially those using gapped k-mers as features (gk), have obtained great success in classifying sequences like DNA, protein, and text. However, the state-of-the-art gk-SK runs extremely slow when we increase the dictionary size ({Sigma}) or allow more mismatches (M). This is because current gk-SK uses a trie-based algorithm to calculate co-occurrence of mismatched substrings resulting in a time cost proportional to O({Sigma}M). We propose a fast algorithm for calculating Gapped k-mer Kernel using Counting (GaKCo). GaKCo uses associative arrays to calculate the co-occurrence of substrings using cumulative counting. This algorithm is fast, scalable to larger{Sigma} and M, and naturally parallelizable. We provide a rigorous asymptotic analysis that compares GaKCo with the state-of-the-art gk-SK. Theoretically, the time cost of GaKCo is independent of the{Sigma} M term that slows down the trie-based approach. Experimentally, we observe that GaKCo achieves the same accuracy as the state-of-the-art and outperforms its speed by factors of 2, 100, and 4, on classifying sequences of DNA (5 datasets), protein (12 datasets), and character-based English text (2 datasets). 1

bioinformatics↗

bioRxiv2018

Phosphoserine acidic cluster motifs in the cytoplasmic domains of transmembrane proteins bind distinct basic regions on the μ subunits of clathrin adaptor protein complexes

Protein trafficking in the endosomal system involves the recognition of specific signals within the cytoplasmic domains (CDs) of transmembrane proteins by clathrin adaptors. One such signal is the phosphoserine acidic cluster (PSAC), the prototype of which is in the endoprotease Furin. How PSACs are recognized by clathrin adaptors has been controversial. We reported previously that HIV-1 Vpu, which modulates cellular immunoreceptors, contains a PSAC that binds to the {micro} subunits of clathrin adaptor protein (AP) complexes. Here, we show that the CD of Furin binds the {micro} subunits of AP-1 and AP-2 in a phosphorylation-dependent manner. Moreover, we identify a PSAC in a cytoplasmic loop of the cellular transmembrane Serinc3, an inhibitor of the infectivity of retroviruses. The two serines within the PSAC of Serinc3 are phosphorylated by casein kinase II and mediate interaction with the {micro} subunits in vitro. The sites of these serines vary among mammals in a manner consistent with host-pathogen conflict, yet the Serinc3-PSAC seems dispensible for anti-HIV activity and for counteraction by HIV-1 Nef. The CDs of Vpu, Furin, and the PSAC-containing loop of Serinc3 each bind the subunit of AP-2 ({micro}2) with similar affinities, but they appear to utilize different basic regions on {micro}2. The Serinc3 loop requires a region previously reported to bind the acidic plasma membrane lipid phosphatidylinositol-4,5-bisphosphate. These data suggest that the PSACs within different proteins recognize different basic regions on the {micro} surface, providing the potential to inhibit the activity of viral proteins without necessarily affecting cellular protein trafficking.

biochemistry↗

bioRxiv2017

What are the most influencing factors in reconstructing a reliable transcriptome assembly?

Reconstructing the genome and transcriptome for a new or extant species are essential steps in expanding our understanding of the organisms active RNA landscape and gene regulatory dynamics, as well as for developing therapeutic targets to fight disease. The advancement of sequencing technologies has paved the way to generate high-quality draft transcriptomes. With many possible approaches available to accomplish this task, there is a need for a closer investigation of the factors that influence the quality of the results. We carried out an extensive survey of variety of elements that are important in transcriptome assembly. We utilized the human RNA-Seq data from the Sequencing Quality Control Consortium (SEQC) as a well-characterized and comprehensive resource with an available, well-studied human reference genome. Our results indicate that the quality of the library construction significantly impacts the quality of the assembly. Higher coverage of the genome is not as important as the quality of the input RNA-Seq data. Thus, once a certain coverage is attained, the quality of the assembly is mainly dependent on the base-calling accuracy of the input sequencing reads; and it is important to avoid saturating the assembler with extra coverage.

bioinformatics↗

bioRxiv2017

Improving microbial electrosynthesis of polyhydroxybutyrate (PHB) from CO2 by Rhodopseudomonas palustris TIE-1 using an immobilized iron complex modified cathode

Microbial electrosynthesis (MES) is a promising bioelectrochemical approach to produce biochemicals. A previous study showed that Rhodopseudomonas palustris TIE-1 can directly use poised electrodes as electron donors for photoautotrophic growth at cathodic potentials that avoid electrolytic H2 production (photoelectroautotrophy). To make TIE-1 an effective biocatalyst for MES, we need to improve its electron uptake ability and growth under photoelectroautotrophic conditions. Because TIE-1 interacts with various forms of iron while using it as a source of electrons for photoautotrophy (photoferrotrophy), we tested the ability of iron-based redox mediators to enhance direct electron uptake. Our data show that soluble iron cannot act as a redox mediator for electron uptake by TIE-1 from a cathode poised at +100mV vs. Standard Hydrogen electrode. We then tested whether an immobilized iron-based redox mediator Prussian Blue (PB) can enhance electron uptake by TIE-1. Chronoamperometry indicates that cathodic current uptake by TIE-1 increased from 1.47 {+/-} 0.04 to 5.6 {+/-} 0.09 {micro}A/cm2 (3.8 times) and the production of the bioplastic, polyhydroxybutyrate (PHB) improved from 13.5 {+/-} 0.2 g/L to 18.8 {+/-} 0.5 g/L (1.4 times) on electrodes coated with PB. Overall, our data show that immobilized PB can increase direct electron uptake by TIE-1 and enhances PHB production.

microbiology↗

bioRxiv2017

Towards sustainable bioplastic production in resource limited environments using the photoferroautotrophic and photoelectroautotrophic bacterium Rhodopseudomonas palustris TIE-1

Bioplastics are an attractive alternative to petroleum-derived plastics because of the harmful environmental effects of conventional plastics and the impending fossil fuel crisis. Polyhydroxybutyrate (PHB) is a well-known bioplastic that is produced by several microbes using organic carbon sources. Autotrophic (using carbon dioxide or CO2) PHB production is reported for only a few organisms. Sustainable PHB bioproduction using other autotrophic microbes needs to be explored. Rhodopseudomonas palustris, a metabolically versatile purple non-sulfur bacterium (PNSB) is known to produce PHBs under photoheterotrophic conditions. Rhodopseudomonas palustris strain TIE-1 demonstrates extended metabolic versatility by using electron sources such as ferrous iron and poised electrodes for photoautotrophy. Here we report the ability of TIE-1 to produce PHB under photoferroautotrophic (light - energy source, ferrous iron - electron source and CO2 - carbon source) and photoelectroautotrophic (light - energy source, poised electrodes - electron source and CO2 - carbon source) growth conditions. PHB accumulation was observed both under nitrogen (N2) fixing and non-N2 fixing conditions. For comparison, we determined PHB production under chemoheterotrophic, photoheterotrophic and photoautotrophic conditions using hydrogen as the electron donor. Photoferroautotrophic and photoelectroautotrophic PHB production was on par with that observed from organic carbon substrates such as butyrate. PHB production increased during N2 fixation under photoheterotrophic conditions but not during photoautotrophic growth. Electron microscopy confirmed that TIE-1 cells accumulate PHBs internally under the conditions that showed highest production. However, gene expression analysis suggests that PHB cycle genes are not differentially regulated despite observable changes in biopolymer production.

microbiology↗

bioRxiv2017

POWERDRESS-mediated histone deacetylation is essential for thermomorphogenesis in Arabidopsis thaliana

Ambient temperature influences plant growth and development and minor changes can substantially impact crop yields. The underlying mechanisms for temperature perception and response are just beginning to emerge. Chromatin remodeling via the eviction of the histone variant H2A.Z in nucleosomes that alters gene expression is a critical component of thermal response in plants. However, whether chromatin-remodeling processes such as histone modifications play a global role in thermal response remains unknown. Using a combination of genetic analysis, chemical inhibition studies and RNA-seq analysis coupled with meta-analysis, here we identify POWERDRESS (PWR), a SANT-domain containing protein that is known to interact with HISTONE DEACETYLASE 9 (HDA9), as a novel key factor required for thermomorphogenesis in Arabidopsis thaliana. We identify that mutations in PWR impede thermomorphogenesis exemplified by severely attenuated temperature-induced hypocotyl/petiole elongation and early flowering. We show that inhibitors of histone deacetylases diminish temperature-induced hypocotyl elongation, which demonstrates for the first time a requirement for histone deacetylation in thermomorphogenesis. Genes that are misregulated in pwr mutants showed enrichment for GO terms associated with \"response\". Our expression studies coupled with meta-analysis revealed a significant overlap between genes misregulated in pwr mutants and genes that are enriched for H2A.Z in their gene bodies. Meta-analyses reveal that genes misregulated in pwr mutants in diverse conditions also overlap with genes that are differentially expressed in the mutants of the components of the SWR1 complex that mediates H2A.Z nucleosome dynamics. Our findings thus uncover a role for PWR in facilitating thermal response and suggest a potential link between histone deacetylation and H2A.Z nucleosome dynamics in regulation of gene expression in plants.\n\nAuthor summaryPlant growth and development is influenced by a variety of external environmental cues. Ambient temperature affects almost all stages of plant development but the underlying molecular mechanisms remain largely unknown. In this paper, the authors show that histone deacetylation, one of the major chromatin remodeling processes, is essential for eliciting growth temperature-induced responses in plants. The authors identify POWERDRESS, a protein known to interact with HISTONE DEACETYLASE 9, as a novel key player essential for eliciting high temperature induced responses in Arabidopsis. Another chromatin remodeling mechanism that is known to play a role in thermal response is the eviction of histone variant H2A.Z from nucleosomes. Through transcriptome studies the authors demonstrate an overlap between gene regulations conferred through PWR-mediated histone H3 deacetylation and that conferred via histone H2A.Z eviction/incorporation dynamics. This study identifies a key novel gene that is essential for plants to elicit high temperature responses and reveals close links between two seemingly distinct chromatin-remodeling processes in regulating gene expression in plants.

genetics↗

bioRxiv2017

Chitosan perception in Arabidopsis requires the chitin receptor AtCERK1 suggesting an improved model for receptor structure and function

Chitin, a linear polymer of N-acetyl-D-glucosamine, and chitosans, fully or partially deacetylated derivatives of chitin, are known to elicit defense reactions in higher plants. We compared the ability of chitin and chitosan oligomers and polymers (chitin oligomers with degree of polymerization 3 to 8; chitosan oligomers with degree of acetylation 0% to 35% and degree of polymerization 3 to 15; chitosan polymers with degree of acetylation 1% to 60% and degree of polymerization ~1300) to elicit an oxidative burst indicative of induced defense reactions in A. thaliana seedlings. Fully deacetylated chitosans were not able to trigger a response; elicitor activity increased with increasing degree of acetylation of chitosan polymers. Partially acetylated chitosan oligomers required a minimum degree of polymerization of 6 and at least four N-acetyl groups to trigger a response. Invariably, elicitation of an oxidative burst required the presence of the chitin receptor AtCERK1. Our results as well as previously published studies on chitin and chitosan perception in plants are best explained by a new general model of LysM-containing receptor complexes where two partners form a long, but off-set chitin-binding groove and are, thus, dimerized by one chitin or chitosan molecule, sharing a central GlcNAc unit with which both LysM domains interact. To verify this model and to distinguish it from earlier models, we assayed elicitor and inhibitor activities of selected partially acetylated chitosan oligomers with fully defined structures. In contrast to the initial \"continuous groove\", the original \"sandwich\", or the current \"sliding mode\" models for the chitin/chitosan receptor, the here proposed \"slipped sandwich\" model - which builds on these earlier models and represents a consensus combination of these - is in agreement with all experimental observations.

biochemistry↗

bioRxiv2017

A Chiral Selectivity Relaxed Paralog Of DTD For Proofreading tRNA Mischarging In Animalia

D-aminoacyl-tRNA deacylase (DTD), a trans-editing factor found in bacteria and eukaryotes, removes D-amino acids mischarged on tRNAs as well as achiral glycine mischarged on tRNAAla. An invariant cross-subunit Gly-cisPro motif forms the mechanistic basis of strict L-amino acid rejection from the catalytic site. Here, we present the identification of a DTD variant, named ATD (Animalia-specific tRNA deacylase), that harbors a Gly-transPro motif. The cis-to-trans switch causes a \"gain of function\" through L-chiral selectivity in ATD resulting in the clearing of L-alanine mischarged on tRNAThr(G4*U69) by eukaryotic AlaRS. The biochemical proofreading activity of ATD is conserved across diverse classes of phylum Chordata. Animalia genomes enriched in tRNAThr(G4*U69) genes are in strict association with the presence of ATD, underlining the mandatory requirement of a dedicated factor to proofread tRNA misaminoacylation. The study highlights the emergence of ATD during genome expansion as a key event associated with the evolution of Animalia.

biochemistry↗